diff --git a/modules/io/pymod/export_omf_io.cc b/modules/io/pymod/export_omf_io.cc
index 480095319e8b2f1e229a3b8ee3de07bbbbeb5e91..ba10cfb6cafb7f43e7cd98502021dc530f3e7f00 100644
--- a/modules/io/pymod/export_omf_io.cc
+++ b/modules/io/pymod/export_omf_io.cc
@@ -39,9 +39,19 @@ namespace{
}
void export_omf_io() {
+
+ enum_<OMF::OMFOption>("OMFOption")
+ .value("DEFAULT_PEPLIB", OMF::DEFAULT_PEPLIB)
+ .value("LOSSY", OMF::LOSSY)
+ .value("AVG_BFACTORS", OMF::AVG_BFACTORS)
+ .value("ROUND_BFACTORS", OMF::ROUND_BFACTORS)
+ .value("SKIP_SS", OMF::SKIP_SS)
+ .value("INFER_PEP_BONDS", OMF::INFER_PEP_BONDS)
+ ;
+
class_<OMF, OMFPtr>("OMF",no_init)
- .def("FromEntity", &OMF::FromEntity).staticmethod("FromEntity")
- .def("FromMMCIF", &OMF::FromMMCIF).staticmethod("FromMMCIF")
+ .def("FromEntity", &OMF::FromEntity, (arg("ent"), arg("options")=0)).staticmethod("FromEntity")
+ .def("FromMMCIF", &OMF::FromMMCIF, (arg("ent"), arg("mmcif_info"), arg("options")=0)).staticmethod("FromMMCIF")
.def("FromFile", &OMF::FromFile).staticmethod("FromFile")
.def("FromBytes", &wrap_from_bytes).staticmethod("FromBytes")
.def("ToFile", &OMF::ToFile)
diff --git a/modules/io/src/mol/omf.cc b/modules/io/src/mol/omf.cc
index 3d3c144deb6d9a962c5178a1779c804fa2cb9705..2de1e477f116633ece80e044e1b715f768955e50 100644
--- a/modules/io/src/mol/omf.cc
+++ b/modules/io/src/mol/omf.cc
@@ -5,7 +5,6 @@
#include "omf.hh"
-
namespace{
// some hash function we need for an unordered_map
@@ -303,25 +302,33 @@ namespace{
// dump and load maps with string as key and ChainDataPtr as value
void Load(std::istream& stream,
- std::map<String, ost::io::ChainDataPtr>& map) {
+ std::map<String, ost::io::ChainDataPtr>& map,
+ const std::vector<ost::io::ResidueDefinition>& res_def,
+ bool lossy, bool avg_bfactors, bool round_bfactors,
+ bool skip_ss) {
uint32_t size;
stream.read(reinterpret_cast<char*>(&size), sizeof(uint32_t));
map.clear();
for(uint i = 0; i < size; ++i) {
ost::io::ChainDataPtr p(new ost::io::ChainData);
- p->FromStream(stream);
+ p->FromStream(stream, res_def, lossy, avg_bfactors, round_bfactors,
+ skip_ss);
map[p->ch_name] = p;
}
}
void Dump(std::ostream& stream,
- const std::map<String, ost::io::ChainDataPtr>& map) {
+ const std::map<String, ost::io::ChainDataPtr>& map,
+ const std::vector<ost::io::ResidueDefinition>& res_def,
+ bool lossy, bool avg_bfactors, bool round_bfactors,
+ bool skip_ss) {
uint32_t size = map.size();
stream.write(reinterpret_cast<char*>(&size), sizeof(uint32_t));
for(auto it = map.begin(); it != map.end(); ++it) {
// we don't dump the key (chain name), that's an attribute of the
// chain itself anyway
- it->second->ToStream(stream);
+ it->second->ToStream(stream, res_def, lossy, avg_bfactors,
+ round_bfactors, skip_ss);
}
}
@@ -516,36 +523,47 @@ namespace{
Dump(stream, run_length_encoded);
}
- void LoadPosVec(std::istream& stream, std::vector<Real>& vec) {
+ void LoadPosVec(std::istream& stream, std::vector<Real>& vec, bool lossy) {
std::vector<int> delta_encoded;
Load(stream, delta_encoded);
std::vector<int> int_vec;
DeltaDecoding(delta_encoded, int_vec);
- IntToRealVec(int_vec, vec, 0.001);
+ if(lossy) {
+ IntToRealVec(int_vec, vec, 0.1);
+ } else {
+ IntToRealVec(int_vec, vec, 0.001);
+ }
}
- void LoadPositions(std::istream& stream, geom::Vec3List& positions) {
+ void LoadPositions(std::istream& stream, geom::Vec3List& positions,
+ bool lossy) {
std::vector<Real> x_pos;
std::vector<Real> y_pos;
std::vector<Real> z_pos;
- LoadPosVec(stream, x_pos);
- LoadPosVec(stream, y_pos);
- LoadPosVec(stream, z_pos);
+ LoadPosVec(stream, x_pos, lossy);
+ LoadPosVec(stream, y_pos, lossy);
+ LoadPosVec(stream, z_pos, lossy);
positions.resize(x_pos.size());
for(uint i = 0; i < positions.size(); ++i) {
positions[i] = geom::Vec3(x_pos[i], y_pos[i], z_pos[i]);
}
}
- void DumpPosVec(std::ostream& stream, const std::vector<Real>& vec) {
+ void DumpPosVec(std::ostream& stream, const std::vector<Real>& vec,
+ bool lossy) {
std::vector<int> int_vec;
- RealToIntVec(vec, int_vec, 1000);
+ if(lossy) {
+ RealToIntVec(vec, int_vec, 10);
+ } else {
+ RealToIntVec(vec, int_vec, 1000);
+ }
std::vector<int> delta_compressed;
DeltaEncoding(int_vec, delta_compressed);
Dump(stream, delta_compressed);
}
- void DumpPositions(std::ostream& stream, const geom::Vec3List& positions) {
+ void DumpPositions(std::ostream& stream, const geom::Vec3List& positions,
+ bool lossy) {
std::vector<Real> x_pos(positions.size());
std::vector<Real> y_pos(positions.size());
std::vector<Real> z_pos(positions.size());
@@ -554,12 +572,13 @@ namespace{
y_pos[i] = positions[i][1];
z_pos[i] = positions[i][2];
}
- DumpPosVec(stream, x_pos);
- DumpPosVec(stream, y_pos);
- DumpPosVec(stream, z_pos);
+ DumpPosVec(stream, x_pos, lossy);
+ DumpPosVec(stream, y_pos, lossy);
+ DumpPosVec(stream, z_pos, lossy);
}
- void LoadBFactors(std::istream& stream, std::vector<Real>& bfactors) {
+ void LoadBFactors(std::istream& stream, std::vector<Real>& bfactors,
+ bool round_bfactors) {
int8_t bfactor_encoding = 0;
stream.read(reinterpret_cast<char*>(&bfactor_encoding), sizeof(int8_t));
@@ -568,21 +587,34 @@ namespace{
Load(stream, delta_encoded);
std::vector<int> int_vec;
DeltaDecoding(delta_encoded, int_vec);
- IntToRealVec(int_vec, bfactors, 0.01);
+ if(round_bfactors) {
+ IntToRealVec(int_vec, bfactors, 1.0);
+ } else {
+ IntToRealVec(int_vec, bfactors, 0.01);
+ }
} else if(bfactor_encoding == 42) {
std::vector<int> runlength_encoded;
Load(stream, runlength_encoded);
std::vector<int> int_vec;
RunLengthDecoding(runlength_encoded, int_vec);
- IntToRealVec(int_vec, bfactors, 0.01);
+ if(round_bfactors) {
+ IntToRealVec(int_vec, bfactors, 1.0);
+ } else {
+ IntToRealVec(int_vec, bfactors, 0.01);
+ }
} else {
throw ost::Error("Observed invalid bfactor encoding");
}
}
- void DumpBFactors(std::ostream& stream, const std::vector<Real>& bfactors) {
+ void DumpBFactors(std::ostream& stream, const std::vector<Real>& bfactors,
+ bool round_bfactors) {
std::vector<int> int_vec;
- RealToIntVec(bfactors, int_vec, 100);
+ if(round_bfactors) {
+ RealToIntVec(bfactors, int_vec, 1);
+ } else {
+ RealToIntVec(bfactors, int_vec, 100);
+ }
// Hack: some structures (e.g. EM) have all bfactors set to 0.0
// this efficiently compresses with runlength encoding.
@@ -850,35 +882,2147 @@ ChainData::ChainData(const ost::mol::ChainHandle& chain,
}
}
-void ChainData::ToStream(std::ostream& stream) const {
+void ChainData::ToStream(std::ostream& stream,
+ const std::vector<ResidueDefinition>& res_def,
+ bool lossy, bool avg_bfactors,
+ bool round_bfactors, bool skip_ss) const {
Dump(stream, ch_name);
DumpResDefIndices(stream, res_def_indices);
DumpRnums(stream, rnums);
DumpInsertionCodes(stream, insertion_codes);
DumpOccupancies(stream, occupancies);
- DumpBFactors(stream, bfactors);
- DumpPositions(stream, positions);
+ if(avg_bfactors) {
+ std::vector<Real> tmp;
+ int start = 0;
+ for(auto it = res_def_indices.begin(); it != res_def_indices.end(); ++it) {
+ int len = res_def[*it].anames.size();
+ int end = start + len;
+ Real avg = 0.0;
+ for(int i = start; i < end; ++i) {
+ avg += bfactors[i];
+ }
+ if(len > 0) {
+ avg /= len;
+ }
+ tmp.push_back(avg);
+ start += len;
+ }
+ DumpBFactors(stream, tmp, round_bfactors);
+ } else {
+ DumpBFactors(stream, bfactors, round_bfactors);
+ }
+
+ DumpPositions(stream, positions, lossy);
DumpBonds(stream, bonds);
DumpBondOrders(stream, bond_orders);
- DumpIntVec(stream, sec_structures);
+ if(!skip_ss) {
+ DumpIntVec(stream, sec_structures);
+ }
}
-void ChainData::FromStream(std::istream& stream) {
+void ChainData::FromStream(std::istream& stream,
+ const std::vector<ResidueDefinition>& res_def,
+ bool lossy, bool avg_bfactors, bool round_bfactors,
+ bool skip_ss) {
+
Load(stream, ch_name);
LoadResDefIndices(stream, res_def_indices);
LoadRnums(stream, rnums);
LoadInsertionCodes(stream, insertion_codes);
LoadOccupancies(stream, occupancies);
- LoadBFactors(stream, bfactors);
- LoadPositions(stream, positions);
+ if(avg_bfactors) {
+ std::vector<Real> tmp;
+ LoadBFactors(stream, tmp, round_bfactors);
+ for(size_t i = 0; i < res_def_indices.size(); ++i) {
+ int len = res_def[res_def_indices[i]].anames.size();
+ Real bfac = tmp[i];
+ bfactors.insert(bfactors.end(), len, bfac);
+ }
+ } else {
+ LoadBFactors(stream, bfactors, round_bfactors);
+ }
+ LoadPositions(stream, positions, lossy);
LoadBonds(stream, bonds);
LoadBondOrders(stream, bond_orders);
- LoadIntVec(stream, sec_structures);
+ if(skip_ss) {
+ sec_structures.assign(res_def_indices.size(), 'C');
+ } else {
+ LoadIntVec(stream, sec_structures);
+ }
}
-OMFPtr OMF::FromEntity(const ost::mol::EntityHandle& ent) {
+DefaultPepLib::DefaultPepLib() {
+
+ /* hardcoded constructor created with:
+
+ from ost import conop
+ def ProcessCompound(comp_name, lib, skip_oxt=True):
+ c = lib.FindCompound(comp_name)
+ anames = list()
+ idx_mapper = dict()
+ element_mapper = dict()
+ for a_idx, a in enumerate(c.atom_specs):
+ if a.element == "H":
+ continue
+ if skip_oxt and a.name == "OXT":
+ continue
+ idx_mapper[a_idx] = a.name
+ anames.append(a.name)
+ element_mapper[a.name] = a.element
+ anames.sort()
+ bond_data = list()
+ for b in c.bond_specs:
+ idx_one = b.atom_one
+ idx_two = b.atom_two
+ if idx_one in idx_mapper and idx_two in idx_mapper:
+ aname_one = idx_mapper[idx_one]
+ aname_two = idx_mapper[idx_two]
+ idx_one = anames.index(aname_one)
+ idx_two = anames.index(aname_two)
+ if idx_one < idx_two:
+ bond_data.append(((idx_one, idx_two), b.order))
+ else:
+ bond_data.append(((idx_two, idx_one), b.order))
+ bond_data.sort()
+ print(f" res_def = ResidueDefinition();")
+ print(f" res_def.name = \"{comp_name}\";")
+ print(f" res_def.olc = '{c.GetOneLetterCode()}';")
+ print(f" res_def.chem_type = '{c.chem_type}';")
+ print(f" res_def.chem_class = '{c.chem_class}';")
+ for aname in anames:
+ print(f" res_def.anames.push_back(\"{aname}\");")
+ for aname in anames:
+ print(f" res_def.elements.push_back(\"{element_mapper[aname]}\");")
+ print(f" res_def.is_hetatm.assign({len(anames)}, false);")
+ for b in bond_data:
+ print(f" res_def.bonds.push_back({b[0][0]});")
+ print(f" res_def.bonds.push_back({b[0][1]});")
+ for b in bond_data:
+ print(f" res_def.bond_orders.push_back({b[1]});")
+ print(" residue_definitions.push_back(res_def);")
+ print()
+ lib = conop.GetDefaultLib()
+ anames = ["ALA", "ARG", "ASN", "ASP", "GLN", "GLU", "LYS", "SER", "CYS", "MET",
+ "TRP", "TYR", "THR", "VAL", "ILE", "LEU", "GLY", "PRO", "HIS", "PHE"]
+ print(" ResidueDefinition res_def;");
+ for aname in anames:
+ ProcessCompound(aname, lib)
+ ProcessCompound(aname, lib, skip_oxt = False)
+ */
+
+ ResidueDefinition res_def;
+ res_def = ResidueDefinition();
+ res_def.name = "ALA";
+ res_def.olc = 'A';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(5, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(3);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "ALA";
+ res_def.olc = 'A';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OXT");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(6, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(3);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "ARG";
+ res_def.olc = 'R';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("CZ");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("NE");
+ res_def.anames.push_back("NH1");
+ res_def.anames.push_back("NH2");
+ res_def.anames.push_back("O");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(11, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(10);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(9);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "ARG";
+ res_def.olc = 'R';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("CZ");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("NE");
+ res_def.anames.push_back("NH1");
+ res_def.anames.push_back("NH2");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OXT");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(12, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(10);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(11);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(9);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "ASN";
+ res_def.olc = 'N';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("ND2");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OD1");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(8, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(7);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "ASN";
+ res_def.olc = 'N';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("ND2");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OD1");
+ res_def.anames.push_back("OXT");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(9, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(7);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "ASP";
+ res_def.olc = 'D';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OD1");
+ res_def.anames.push_back("OD2");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(8, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(7);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "ASP";
+ res_def.olc = 'D';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OD1");
+ res_def.anames.push_back("OD2");
+ res_def.anames.push_back("OXT");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(9, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(7);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "GLN";
+ res_def.olc = 'Q';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("NE2");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OE1");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(9, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(8);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "GLN";
+ res_def.olc = 'Q';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("NE2");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OE1");
+ res_def.anames.push_back("OXT");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(10, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(9);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(8);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "GLU";
+ res_def.olc = 'E';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OE1");
+ res_def.anames.push_back("OE2");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(9, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(8);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "GLU";
+ res_def.olc = 'E';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OE1");
+ res_def.anames.push_back("OE2");
+ res_def.anames.push_back("OXT");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(10, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(9);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(8);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "LYS";
+ res_def.olc = 'K';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD");
+ res_def.anames.push_back("CE");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("NZ");
+ res_def.anames.push_back("O");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(9, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(7);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "LYS";
+ res_def.olc = 'K';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD");
+ res_def.anames.push_back("CE");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("NZ");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OXT");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(10, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(9);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(7);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "SER";
+ res_def.olc = 'S';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OG");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(6, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(5);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "SER";
+ res_def.olc = 'S';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OG");
+ res_def.anames.push_back("OXT");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(7, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(5);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "CYS";
+ res_def.olc = 'C';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("SG");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("S");
+ res_def.is_hetatm.assign(6, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(5);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "CYS";
+ res_def.olc = 'C';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OXT");
+ res_def.anames.push_back("SG");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("S");
+ res_def.is_hetatm.assign(7, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(6);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "MET";
+ res_def.olc = 'M';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CE");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("SD");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("S");
+ res_def.is_hetatm.assign(8, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(7);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "MET";
+ res_def.olc = 'M';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CE");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OXT");
+ res_def.anames.push_back("SD");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("S");
+ res_def.is_hetatm.assign(9, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(8);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "TRP";
+ res_def.olc = 'W';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD1");
+ res_def.anames.push_back("CD2");
+ res_def.anames.push_back("CE2");
+ res_def.anames.push_back("CE3");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("CH2");
+ res_def.anames.push_back("CZ2");
+ res_def.anames.push_back("CZ3");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("NE1");
+ res_def.anames.push_back("O");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(14, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(13);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(11);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(12);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(9);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(12);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(10);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(9);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(10);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "TRP";
+ res_def.olc = 'W';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD1");
+ res_def.anames.push_back("CD2");
+ res_def.anames.push_back("CE2");
+ res_def.anames.push_back("CE3");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("CH2");
+ res_def.anames.push_back("CZ2");
+ res_def.anames.push_back("CZ3");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("NE1");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OXT");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(15, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(13);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(14);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(11);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(12);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(9);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(12);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(10);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(9);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(10);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "TYR";
+ res_def.olc = 'Y';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD1");
+ res_def.anames.push_back("CD2");
+ res_def.anames.push_back("CE1");
+ res_def.anames.push_back("CE2");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("CZ");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OH");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(12, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(10);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(9);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(11);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "TYR";
+ res_def.olc = 'Y';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD1");
+ res_def.anames.push_back("CD2");
+ res_def.anames.push_back("CE1");
+ res_def.anames.push_back("CE2");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("CZ");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OH");
+ res_def.anames.push_back("OXT");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(13, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(10);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(12);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(9);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(11);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "THR";
+ res_def.olc = 'T';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CG2");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OG1");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(7, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(6);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "THR";
+ res_def.olc = 'T';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CG2");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OG1");
+ res_def.anames.push_back("OXT");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(8, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(6);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "VAL";
+ res_def.olc = 'V';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CG1");
+ res_def.anames.push_back("CG2");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(7, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(4);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "VAL";
+ res_def.olc = 'V';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CG1");
+ res_def.anames.push_back("CG2");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OXT");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(8, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(4);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "ILE";
+ res_def.olc = 'I';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD1");
+ res_def.anames.push_back("CG1");
+ res_def.anames.push_back("CG2");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(8, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(4);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "ILE";
+ res_def.olc = 'I';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD1");
+ res_def.anames.push_back("CG1");
+ res_def.anames.push_back("CG2");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OXT");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(9, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(4);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "LEU";
+ res_def.olc = 'L';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD1");
+ res_def.anames.push_back("CD2");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(8, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(5);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "LEU";
+ res_def.olc = 'L';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD1");
+ res_def.anames.push_back("CD2");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OXT");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(9, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(5);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "GLY";
+ res_def.olc = 'G';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'P';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(4, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "GLY";
+ res_def.olc = 'G';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'P';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OXT");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(5, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "PRO";
+ res_def.olc = 'P';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(7, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(5);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "PRO";
+ res_def.olc = 'P';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OXT");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(8, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(5);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "HIS";
+ res_def.olc = 'H';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD2");
+ res_def.anames.push_back("CE1");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("ND1");
+ res_def.anames.push_back("NE2");
+ res_def.anames.push_back("O");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(10, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(9);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(7);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "HIS";
+ res_def.olc = 'H';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD2");
+ res_def.anames.push_back("CE1");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("ND1");
+ res_def.anames.push_back("NE2");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OXT");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(11, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(9);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(10);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(7);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "PHE";
+ res_def.olc = 'F';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD1");
+ res_def.anames.push_back("CD2");
+ res_def.anames.push_back("CE1");
+ res_def.anames.push_back("CE2");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("CZ");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(11, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(10);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(9);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(8);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+
+ res_def = ResidueDefinition();
+ res_def.name = "PHE";
+ res_def.olc = 'F';
+ res_def.chem_type = 'A';
+ res_def.chem_class = 'L';
+ res_def.anames.push_back("C");
+ res_def.anames.push_back("CA");
+ res_def.anames.push_back("CB");
+ res_def.anames.push_back("CD1");
+ res_def.anames.push_back("CD2");
+ res_def.anames.push_back("CE1");
+ res_def.anames.push_back("CE2");
+ res_def.anames.push_back("CG");
+ res_def.anames.push_back("CZ");
+ res_def.anames.push_back("N");
+ res_def.anames.push_back("O");
+ res_def.anames.push_back("OXT");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("C");
+ res_def.elements.push_back("N");
+ res_def.elements.push_back("O");
+ res_def.elements.push_back("O");
+ res_def.is_hetatm.assign(12, false);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(10);
+ res_def.bonds.push_back(0);
+ res_def.bonds.push_back(11);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(1);
+ res_def.bonds.push_back(9);
+ res_def.bonds.push_back(2);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(3);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(4);
+ res_def.bonds.push_back(7);
+ res_def.bonds.push_back(5);
+ res_def.bonds.push_back(8);
+ res_def.bonds.push_back(6);
+ res_def.bonds.push_back(8);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ res_def.bond_orders.push_back(2);
+ res_def.bond_orders.push_back(1);
+ residue_definitions.push_back(res_def);
+}
+
+OMFPtr OMF::FromEntity(const ost::mol::EntityHandle& ent,
+ uint8_t options) {
OMFPtr omf(new OMF);
+ omf->options_ = options;
//////////////////////////////////////////////////////////////////////////////
// Generate kind of a "mini compound library"... Eeach unique residue gets //
@@ -887,8 +3031,18 @@ OMFPtr OMF::FromEntity(const ost::mol::EntityHandle& ent) {
std::unordered_map<ResidueDefinition, int, ResidueDefinitionHash> res_def_map;
std::unordered_map<unsigned long, int> res_idx_map;
- ost::mol::ResidueHandleList res_list = ent.GetResidueList();
int idx = 0;
+
+ if(omf->OptionSet(DEFAULT_PEPLIB)) {
+ omf->residue_definitions_ = DefaultPepLib::Instance().residue_definitions;
+ for(auto it = omf->residue_definitions_.begin();
+ it != omf->residue_definitions_.end(); ++it) {
+ res_def_map[*it] = idx;
+ ++idx;
+ }
+ }
+
+ ost::mol::ResidueHandleList res_list = ent.GetResidueList();
for(auto it = res_list.begin(); it != res_list.end(); ++it) {
ResidueDefinition def(*it);
auto map_it = res_def_map.find(def);
@@ -935,14 +3089,33 @@ OMFPtr OMF::FromEntity(const ost::mol::EntityHandle& ent) {
for(auto bond_it = bond_list.begin(); bond_it != bond_list.end(); ++bond_it) {
const ost::mol::AtomHandle& at_one = bond_it->GetFirst();
const ost::mol::AtomHandle& at_two = bond_it->GetSecond();
- if(at_one.GetResidue().GetChain() == at_two.GetResidue().GetChain()) {
- if(at_one.GetResidue() != at_two.GetResidue()) {
- int idx = chain_idx_map[at_one.GetResidue().GetChain().GetHashCode()];
- inter_residue_bonds[idx].push_back(std::make_pair(at_one.GetHashCode(),
- at_two.GetHashCode()));
- inter_residue_bond_orders[idx].push_back(bond_it->GetBondOrder());
+ const ost::mol::ResidueHandle& res_one = at_one.GetResidue();
+ const ost::mol::ResidueHandle& res_two = at_two.GetResidue();
+ if(res_one.GetChain() == res_two.GetChain()) {
+ if(res_one != res_two) {
+ if(omf->OptionSet(INFER_PEP_BONDS)) {
+ if(res_one.IsPeptideLinking() && res_two.IsPeptideLinking()) {
+ String aname_one = at_one.GetName();
+ String aname_two = at_two.GetName();
+ if((aname_one == "C" && aname_two == "N" &&
+ res_one.GetNext() == res_two) ||
+ (aname_one == "N" && aname_two == "C" &&
+ res_one.GetPrev() == res_two)) {
+ Real bond_length = bond_it->GetLength();
+ if(bond_length > Real(1.198) && bond_length < Real(1.474)) {
+ // mean bond length (1.336) +- 6 stds (0.023)
+ // this peptide bond can be inferred... skip...
+ continue;
+ }
+ }
+ }
+ }
+ int idx = chain_idx_map[at_one.GetResidue().GetChain().GetHashCode()];
+ inter_residue_bonds[idx].push_back(std::make_pair(at_one.GetHashCode(),
+ at_two.GetHashCode()));
+ inter_residue_bond_orders[idx].push_back(bond_it->GetBondOrder());
}
- } else{
+ } else {
int idx_one = chain_idx_map[at_one.GetResidue().GetChain().GetHashCode()];
int idx_two = chain_idx_map[at_two.GetResidue().GetChain().GetHashCode()];
interchain_bonds.push_back(std::make_pair(at_one.GetHashCode(),
@@ -985,9 +3158,10 @@ OMFPtr OMF::FromEntity(const ost::mol::EntityHandle& ent) {
}
OMFPtr OMF::FromMMCIF(const ost::mol::EntityHandle& ent,
- const MMCifInfo& info) {
+ const MMCifInfo& info,
+ uint8_t options) {
- OMFPtr p = OMF::FromEntity(ent);
+ OMFPtr p = OMF::FromEntity(ent, options);
const std::vector<MMCifInfoBioUnit>& biounits = info.GetBioUnits();
for(auto it = biounits.begin(); it != biounits.end(); ++it) {
p->biounit_definitions_.push_back(BioUnitDefinition(*it));
@@ -1121,13 +3295,25 @@ void OMF::ToStream(std::ostream& stream) const {
uint32_t magic_number = 42;
stream.write(reinterpret_cast<char*>(&magic_number), sizeof(uint32_t));
-
- uint32_t version = 1;
+ uint32_t version = 2;
stream.write(reinterpret_cast<char*>(&version), sizeof(uint32_t));
+ stream.write(reinterpret_cast<const char*>(&options_), sizeof(uint8_t));
+
+ if(OptionSet(DEFAULT_PEPLIB)) {
+ // no need to dump the residue definitions from default lib
+ auto a = residue_definitions_.begin();
+ auto b = residue_definitions_.end();
+ int offset = DefaultPepLib::Instance().residue_definitions.size();
+ std::vector<ResidueDefinition> tmp(a + offset, b);
+ Dump(stream, tmp);
+ }
+ else {
+ Dump(stream, residue_definitions_);
+ }
- Dump(stream, residue_definitions_);
Dump(stream, biounit_definitions_);
- Dump(stream, chain_data_);
+ Dump(stream, chain_data_, residue_definitions_, OptionSet(LOSSY),
+ OptionSet(AVG_BFACTORS), OptionSet(ROUND_BFACTORS), OptionSet(SKIP_SS));
Dump(stream, bond_chain_names_);
Dump(stream, bond_atoms_);
Dump(stream, bond_orders_);
@@ -1143,15 +3329,31 @@ void OMF::FromStream(std::istream& stream) {
uint32_t version;
stream.read(reinterpret_cast<char*>(&version), sizeof(uint32_t));
- if(version != 1) {
+ if(version != 1 && version != 2) {
std::stringstream ss;
- ss << "OST version only supports OMF version 1. Got "<<version;
+ ss << "OST version only supports OMF version 1 and 2. Got "<<version;
throw ost::Error(ss.str());
}
- Load(stream, residue_definitions_);
+ if(version > 1) {
+ stream.read(reinterpret_cast<char*>(&options_), sizeof(uint8_t));
+ }
+
+ if(OptionSet(DEFAULT_PEPLIB)) {
+ // load residue definitions from default lib and append custom definitions
+ std::vector<ResidueDefinition> tmp;
+ Load(stream, tmp);
+ residue_definitions_ = DefaultPepLib::Instance().residue_definitions;
+ residue_definitions_.insert(residue_definitions_.end(),
+ tmp.begin(), tmp.end());
+ }
+ else {
+ Load(stream, residue_definitions_);
+ }
+
Load(stream, biounit_definitions_);
- Load(stream, chain_data_);
+ Load(stream, chain_data_, residue_definitions_, OptionSet(LOSSY),
+ OptionSet(AVG_BFACTORS), OptionSet(ROUND_BFACTORS), OptionSet(SKIP_SS));
Load(stream, bond_chain_names_);
Load(stream, bond_atoms_);
Load(stream, bond_orders_);
@@ -1213,6 +3415,25 @@ void OMF::FillChain(ost::mol::ChainHandle& chain, ost::mol::XCSEditor& ed,
added_atoms[data->bonds[2*bond_idx+1]],
data->bond_orders[bond_idx]);
}
+
+ if(OptionSet(INFER_PEP_BONDS)) {
+ ost::mol::ResidueHandleList res_list = chain.GetResidueList();
+ for(size_t i = 1; i < res_list.size(); ++i) {
+ if(res_list[i-1].IsPeptideLinking() && res_list[i].IsPeptideLinking()) {
+ const ost::mol::AtomHandle& c = res_list[i-1].FindAtom("C");
+ const ost::mol::AtomHandle& n = res_list[i].FindAtom("N");
+ if(c.IsValid() && n.IsValid()) {
+ Real d = geom::Distance(c.GetPos(), n.GetPos());
+ if(d > 0.991 && d < 1.681) {
+ // mean (1.336) +- 15 stds (0.023)
+ // This is an extremely loose threshold but makes sure to also handle
+ // inaccuracies that have been introduced with lossy compression
+ ed.Connect(c, n);
+ }
+ }
+ }
+ }
+ }
}
}} //ns
diff --git a/modules/io/src/mol/omf.hh b/modules/io/src/mol/omf.hh
index ebdaa20d7d9bec28308ad30d5215cc2db2632bb0..a1756bf6112a82cbf33e0101450a6e96cc4253f7 100644
--- a/modules/io/src/mol/omf.hh
+++ b/modules/io/src/mol/omf.hh
@@ -103,9 +103,15 @@ struct ChainData {
const std::vector<int>& inter_residue_bond_orders,
std::unordered_map<long, int>& atom_idx_mapper);
- void ToStream(std::ostream& stream) const;
+ void ToStream(std::ostream& stream,
+ const std::vector<ResidueDefinition>& res_def,
+ bool lossy, bool avg_bfactors, bool round_bfactors,
+ bool skip_ss) const;
- void FromStream(std::istream& stream);
+ void FromStream(std::istream& stream,
+ const std::vector<ResidueDefinition>& res_def,
+ bool lossy, bool avg_bfactors, bool round_bfactors,
+ bool skip_ss);
// chain features
String ch_name;
@@ -127,14 +133,39 @@ struct ChainData {
std::vector<int> bond_orders;
};
+
+class DefaultPepLib{
+public:
+ static DefaultPepLib& Instance() {
+ static DefaultPepLib instance;
+ return instance;
+ }
+ std::vector<ResidueDefinition> residue_definitions;
+
+private:
+ DefaultPepLib();
+ DefaultPepLib(DefaultPepLib const& copy);
+ DefaultPepLib& operator=(DefaultPepLib const& copy);
+};
+
+
class OMF {
public:
- static OMFPtr FromEntity(const ost::mol::EntityHandle& ent);
+ enum OMFOption {DEFAULT_PEPLIB = 1, LOSSY = 2, AVG_BFACTORS = 4,
+ ROUND_BFACTORS = 8, SKIP_SS = 16, INFER_PEP_BONDS = 32};
+
+ bool OptionSet(OMFOption opt) const {
+ return (opt & options_) == opt;
+ }
+
+ static OMFPtr FromEntity(const ost::mol::EntityHandle& ent,
+ uint8_t options = 0);
static OMFPtr FromMMCIF(const ost::mol::EntityHandle& ent,
- const MMCifInfo& info);
+ const MMCifInfo& info,
+ uint8_t options = 0);
static OMFPtr FromFile(const String& fn);
@@ -152,7 +183,7 @@ public:
private:
// only construct with static functions
- OMF() { }
+ OMF(): options_(0) { }
void ToStream(std::ostream& stream) const;
@@ -174,6 +205,9 @@ private:
std::vector<String> bond_chain_names_;
std::vector<int> bond_atoms_;
std::vector<int> bond_orders_;
+
+ // bitfield with options
+ uint8_t options_;
};
}} //ns
diff --git a/modules/io/tests/test_io_omf.py b/modules/io/tests/test_io_omf.py
index 05f8765d951e8530300e529892b35a0547b869f8..bbb954a61f3fae10cc488ebc5d2db3a1d9090c11 100644
--- a/modules/io/tests/test_io_omf.py
+++ b/modules/io/tests/test_io_omf.py
@@ -1,13 +1,16 @@
import unittest
+import math
+
from ost import geom
from ost import io
-def compare_atoms(a1, a2):
- if abs(a1.occupancy - a2.occupancy) > 0.01:
+def compare_atoms(a1, a2, occupancy_thresh = 0.01, bfactor_thresh = 0.01,
+ dist_thresh = 0.001):
+ if abs(a1.occupancy - a2.occupancy) > occupancy_thresh:
return False
- if abs(a1.b_factor - a2.b_factor) > 0.01:
+ if abs(a1.b_factor - a2.b_factor) > bfactor_thresh:
return False
- if geom.Distance(a1.GetPos(), a2.GetPos()) > 0.001:
+ if geom.Distance(a1.GetPos(), a2.GetPos()) > dist_thresh:
return False
if a1.is_hetatom != a2.is_hetatom:
return False
@@ -15,13 +18,16 @@ def compare_atoms(a1, a2):
return False
return True
-def compare_residues(r1, r2):
+def compare_residues(r1, r2, at_occupancy_thresh = 0.01,
+ at_bfactor_thresh = 0.01, at_dist_thresh = 0.001,
+ skip_ss = False):
if r1.GetName() != r2.GetName():
return False
if r1.GetNumber() != r2.GetNumber():
return False
- if str(r1.GetSecStructure()) != str(r2.GetSecStructure()):
- return False
+ if skip_ss is False:
+ if str(r1.GetSecStructure()) != str(r2.GetSecStructure()):
+ return False
if r1.one_letter_code != r2.one_letter_code:
return False
if r1.chem_type != r2.chem_type:
@@ -36,15 +42,24 @@ def compare_residues(r1, r2):
for aname in anames:
a1 = r1.FindAtom(aname)
a2 = r2.FindAtom(aname)
- if not compare_atoms(a1, a2):
+ if not compare_atoms(a1, a2,
+ occupancy_thresh = at_occupancy_thresh,
+ bfactor_thresh = at_bfactor_thresh,
+ dist_thresh = at_dist_thresh):
return False
return True
-def compare_chains(ch1, ch2):
+def compare_chains(ch1, ch2, at_occupancy_thresh = 0.01,
+ at_bfactor_thresh = 0.01, at_dist_thresh = 0.001,
+ skip_ss=False):
if len(ch1.residues) != len(ch2.residues):
return False
for r1, r2 in zip(ch1.residues, ch2.residues):
- if not compare_residues(r1, r2):
+ if not compare_residues(r1, r2,
+ at_occupancy_thresh = at_occupancy_thresh,
+ at_bfactor_thresh = at_bfactor_thresh,
+ at_dist_thresh = at_dist_thresh,
+ skip_ss = skip_ss):
return False
return True
@@ -59,7 +74,9 @@ def compare_bonds(ent1, ent2):
bonds2.append([min(bond_partners), max(bond_partners), b.bond_order])
return sorted(bonds1) == sorted(bonds2)
-def compare_ent(ent1, ent2):
+def compare_ent(ent1, ent2, at_occupancy_thresh = 0.01,
+ at_bfactor_thresh = 0.01, at_dist_thresh = 0.001,
+ skip_ss=False):
chain_names_one = [ch.GetName() for ch in ent1.chains]
chain_names_two = [ch.GetName() for ch in ent2.chains]
if not sorted(chain_names_one) == sorted(chain_names_two):
@@ -68,23 +85,124 @@ def compare_ent(ent1, ent2):
for chain_name in chain_names:
ch1 = ent1.FindChain(chain_name)
ch2 = ent2.FindChain(chain_name)
- if not compare_chains(ch1, ch2):
+ if not compare_chains(ch1, ch2,
+ at_occupancy_thresh = at_occupancy_thresh,
+ at_bfactor_thresh = at_bfactor_thresh,
+ at_dist_thresh = at_dist_thresh,
+ skip_ss=skip_ss):
return False
if not compare_bonds(ent1, ent2):
return False
return True
class TestOMF(unittest.TestCase):
- def test_AU(self):
+
+ def setUp(self):
ent, seqres, info = io.LoadMMCIF("testfiles/mmcif/3T6C.cif.gz",
seqres=True,
info=True)
- omf = io.OMF.FromMMCIF(ent, info)
+ self.ent = ent
+ self.seqres = seqres
+ self.info = info
+
+ def test_AU(self):
+ omf = io.OMF.FromMMCIF(self.ent, self.info)
omf_bytes = omf.ToBytes()
loaded_omf = io.OMF.FromBytes(omf_bytes)
loaded_ent = loaded_omf.GetAU()
- self.assertTrue(compare_ent(ent, loaded_ent))
+ self.assertTrue(compare_ent(self.ent, loaded_ent))
+
+ def test_default_peplib(self):
+ omf = io.OMF.FromMMCIF(self.ent, self.info)
+ omf_bytes = omf.ToBytes()
+ omf_def_pep = io.OMF.FromMMCIF(self.ent, self.info,
+ io.OMFOption.DEFAULT_PEPLIB)
+ omf_def_pep_bytes = omf_def_pep.ToBytes()
+ loaded_omf_def_pep = io.OMF.FromBytes(omf_def_pep_bytes)
+ loaded_ent = loaded_omf_def_pep.GetAU()
+
+ self.assertTrue(len(omf_def_pep_bytes) < len(omf_bytes))
+ self.assertTrue(compare_ent(self.ent, loaded_ent))
+
+ def test_lossy(self):
+ omf = io.OMF.FromMMCIF(self.ent, self.info)
+ omf_bytes = omf.ToBytes()
+ omf_lossy = io.OMF.FromMMCIF(self.ent, self.info,
+ io.OMFOption.LOSSY)
+ omf_lossy_bytes = omf_lossy.ToBytes()
+ loaded_omf_lossy = io.OMF.FromBytes(omf_lossy_bytes)
+ loaded_ent = loaded_omf_lossy.GetAU()
+
+ self.assertTrue(len(omf_lossy_bytes) < len(omf_bytes))
+ self.assertFalse(compare_ent(self.ent, loaded_ent))
+ max_dist = math.sqrt(3*0.05*0.05)
+ self.assertTrue(compare_ent(self.ent, loaded_ent,
+ at_dist_thresh=max_dist))
+
+ def test_avg_bfactors(self):
+ omf = io.OMF.FromMMCIF(self.ent, self.info)
+ omf_bytes = omf.ToBytes()
+ omf_avg_bfac = io.OMF.FromMMCIF(self.ent, self.info,
+ io.OMFOption.AVG_BFACTORS)
+ omf_avg_bfac_bytes = omf_avg_bfac.ToBytes()
+ loaded_omf_avg_bfac = io.OMF.FromBytes(omf_avg_bfac_bytes)
+ loaded_ent = loaded_omf_avg_bfac.GetAU()
+
+ self.assertTrue(len(omf_avg_bfac_bytes) < len(omf_bytes))
+ self.assertFalse(compare_ent(self.ent, loaded_ent))
+ # just give a huge slack for bfactors and check averaging manually
+ self.assertTrue(compare_ent(self.ent, loaded_ent,
+ at_bfactor_thresh=1000))
+
+ self.assertEqual(len(self.ent.residues), len(loaded_ent.residues))
+ for r_ref, r in zip(self.ent.residues, loaded_ent.residues):
+ exp_bfac = sum([a.b_factor for a in r_ref.atoms])
+ exp_bfac /= r_ref.atom_count
+ for a in r.atoms:
+ self.assertTrue(abs(a.b_factor - exp_bfac) < 0.008)
+
+ def test_round_bfactors(self):
+ omf = io.OMF.FromMMCIF(self.ent, self.info)
+ omf_bytes = omf.ToBytes()
+ omf_round_bfac = io.OMF.FromMMCIF(self.ent, self.info,
+ io.OMFOption.ROUND_BFACTORS)
+ omf_round_bfac_bytes = omf_round_bfac.ToBytes()
+ loaded_omf_round_bfac = io.OMF.FromBytes(omf_round_bfac_bytes)
+ loaded_ent = loaded_omf_round_bfac.GetAU()
+
+ self.assertTrue(len(omf_round_bfac_bytes) < len(omf_bytes))
+ self.assertFalse(compare_ent(self.ent, loaded_ent))
+ self.assertTrue(compare_ent(self.ent, loaded_ent,
+ at_bfactor_thresh=0.5))
+
+ def test_skip_ss(self):
+ omf = io.OMF.FromMMCIF(self.ent, self.info)
+ omf_bytes = omf.ToBytes()
+ omf_skip_ss = io.OMF.FromMMCIF(self.ent, self.info,
+ io.OMFOption.SKIP_SS)
+ omf_skip_ss_bytes = omf_skip_ss.ToBytes()
+ loaded_omf_skip_ss = io.OMF.FromBytes(omf_skip_ss_bytes)
+ loaded_ent = loaded_omf_skip_ss.GetAU()
+
+ self.assertTrue(len(omf_skip_ss_bytes) < len(omf_bytes))
+ self.assertFalse(compare_ent(self.ent, loaded_ent))
+ self.assertTrue(compare_ent(self.ent, loaded_ent, skip_ss=True))
+
+ def test_infer_pep_bonds(self):
+ omf = io.OMF.FromMMCIF(self.ent, self.info)
+ omf_bytes = omf.ToBytes()
+ omf_infer_pep_bonds = io.OMF.FromMMCIF(self.ent, self.info,
+ io.OMFOption.INFER_PEP_BONDS)
+ omf_infer_pep_bonds_bytes = omf_infer_pep_bonds.ToBytes()
+ loaded_omf_infer_pep_bonds = io.OMF.FromBytes(omf_infer_pep_bonds_bytes)
+ loaded_ent = loaded_omf_infer_pep_bonds.GetAU()
+
+ self.assertTrue(len(omf_infer_pep_bonds_bytes) < len(omf_bytes))
+ self.assertTrue(compare_ent(self.ent, loaded_ent))
if __name__== '__main__':
- from ost import testutils
- testutils.RunTests()
+ from ost import testutils
+ if testutils.SetDefaultCompoundLib():
+ testutils.RunTests()
+ else:
+ print('No compound library available. Ignoring test_stereochemistry.py tests.')